mirror of
https://github.com/msberends/AMR.git
synced 2026-06-24 10:16:23 +02:00
Built site for AMR@3.0.1.9061: 0c1709c
This commit is contained in:
github-actions
@@ -1,7 +1,7 @@
|
||||
<!DOCTYPE html>
|
||||
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Data Set with 78 679 Taxonomic Records of Microorganisms — microorganisms • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 78 679 Taxonomic Records of Microorganisms — microorganisms"><meta name="description" content="A data set containing the full microbial taxonomy (last updated: June 24th, 2024) of six kingdoms. This data set is the backbone of this AMR package. MO codes can be looked up using as.mo() and microorganism properties can be looked up using any of the mo_* functions.
|
||||
This data set is carefully crafted, yet made 100% reproducible from public and authoritative taxonomic sources (using this script), namely: List of Prokaryotic names with Standing in Nomenclature (LPSN) for bacteria, MycoBank for fungi, and Global Biodiversity Information Facility (GBIF) for all others taxons."><meta property="og:description" content="A data set containing the full microbial taxonomy (last updated: June 24th, 2024) of six kingdoms. This data set is the backbone of this AMR package. MO codes can be looked up using as.mo() and microorganism properties can be looked up using any of the mo_* functions.
|
||||
This data set is carefully crafted, yet made 100% reproducible from public and authoritative taxonomic sources (using this script), namely: List of Prokaryotic names with Standing in Nomenclature (LPSN) for bacteria, MycoBank for fungi, and Global Biodiversity Information Facility (GBIF) for all others taxons."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
|
||||
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Data Set with 96 982 Taxonomic Records of Microorganisms — microorganisms • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.8/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.8/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 96 982 Taxonomic Records of Microorganisms — microorganisms"><meta name="description" content="A data set containing the full microbial taxonomy (last updated: 7th of May, 2026) of 15 kingdoms. This data set is the backbone of this AMR package. MO codes can be looked up using as.mo() and microorganism properties can be looked up using any of the mo_* functions.
|
||||
This data set is carefully crafted, yet made 100% reproducible from public and authoritative taxonomic sources (using this script), namely: List of Prokaryotic names with Standing in Nomenclature (LPSN) for bacteria, MycoBank for fungi, and Global Biodiversity Information Facility (GBIF), via Catalogue of Life (COL) for all others taxons."><meta property="og:description" content="A data set containing the full microbial taxonomy (last updated: 7th of May, 2026) of 15 kingdoms. This data set is the backbone of this AMR package. MO codes can be looked up using as.mo() and microorganism properties can be looked up using any of the mo_* functions.
|
||||
This data set is carefully crafted, yet made 100% reproducible from public and authoritative taxonomic sources (using this script), namely: List of Prokaryotic names with Standing in Nomenclature (LPSN) for bacteria, MycoBank for fungi, and Global Biodiversity Information Facility (GBIF), via Catalogue of Life (COL) for all others taxons."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
|
||||
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
|
||||
|
||||
|
||||
@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9061</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -46,14 +46,14 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
|
||||
</nav><div class="container template-reference-topic">
|
||||
<div class="row">
|
||||
<main id="main" class="col-md-9"><div class="page-header">
|
||||
<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 78 679 Taxonomic Records of Microorganisms</h1>
|
||||
<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 96 982 Taxonomic Records of Microorganisms</h1>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/data.R" class="external-link"><code>R/data.R</code></a></small>
|
||||
<div class="d-none name"><code>microorganisms.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description section level2">
|
||||
<p>A data set containing the full microbial taxonomy (<strong>last updated: June 24th, 2024</strong>) of six kingdoms. This data set is the backbone of this <code>AMR</code> package. MO codes can be looked up using <code><a href="as.mo.html">as.mo()</a></code> and microorganism properties can be looked up using any of the <code><a href="mo_property.html">mo_*</a></code> functions.</p>
|
||||
<p>This data set is carefully crafted, yet made 100% reproducible from public and authoritative taxonomic sources (using <a href="https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_microorganisms.R" class="external-link">this script</a>), namely: <em>List of Prokaryotic names with Standing in Nomenclature (LPSN)</em> for bacteria, <em>MycoBank</em> for fungi, and <em>Global Biodiversity Information Facility (GBIF)</em> for all others taxons.</p>
|
||||
<p>A data set containing the full microbial taxonomy (<strong>last updated: 7th of May, 2026</strong>) of 15 kingdoms. This data set is the backbone of this <code>AMR</code> package. MO codes can be looked up using <code><a href="as.mo.html">as.mo()</a></code> and microorganism properties can be looked up using any of the <code><a href="mo_property.html">mo_*</a></code> functions.</p>
|
||||
<p>This data set is carefully crafted, yet made 100% reproducible from public and authoritative taxonomic sources (using <a href="https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_microorganisms.R" class="external-link">this script</a>), namely: <em>List of Prokaryotic names with Standing in Nomenclature (LPSN)</em> for bacteria, <em>MycoBank</em> for fungi, and <em>Global Biodiversity Information Facility (GBIF), via Catalogue of Life (COL)</em> for all others taxons.</p>
|
||||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
@@ -63,45 +63,27 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
|
||||
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 78 679 observations and 26 variables:</p><ul><li><p><code>mo</code><br> ID of microorganism as used by this package. <em><strong>This is a unique identifier.</strong></em></p></li>
|
||||
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 96 982 observations and 28 variables:</p><ul><li><p><code>mo</code><br> ID of microorganism as used by this package. <em><strong>This is a unique identifier.</strong></em></p></li>
|
||||
<li><p><code>fullname</code><br> Full name, like <code>"Escherichia coli"</code>. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon. <em><strong>This is a unique identifier.</strong></em></p></li>
|
||||
<li><p><code>status</code> <br> Status of the taxon, either <code>"accepted"</code>, <code>"not validly published"</code>, <code>"synonym"</code>, or <code>"unknown"</code></p></li>
|
||||
<li><p><code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br> Taxonomic rank of the microorganism. Note that for fungi, <em>phylum</em> is equal to their taxonomic <em>division</em>. Also, for fungi, <em>subkingdom</em> and <em>subdivision</em> were left out since they do not occur in the bacterial taxonomy.</p></li>
|
||||
<li><p><code>status</code> <br> Status of the taxon, either <code>"accepted"</code>, <code>"synonym"</code>, or <code>"unknown"</code></p></li>
|
||||
<li><p><code>domain</code>, <code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br> Taxonomic rank of the microorganism. Note that for fungi, <em>phylum</em> is used for their taxonomic <em>division</em>. Also, for fungi, <em>subkingdom</em> and <em>subdivision</em> were left out since they do not occur in the bacterial taxonomy. For all species outside the domains of Bacteria and Archaea, the <code>domain</code> and <code>kingdom</code> are identical.</p></li>
|
||||
<li><p><code>rank</code><br> Text of the taxonomic rank of the microorganism, such as <code>"species"</code> or <code>"genus"</code></p></li>
|
||||
<li><p><code>ref</code><br> Author(s) and year of related scientific publication. This contains only the <em>first surname</em> and year of the <em>latest</em> authors, e.g. "Wallis <em>et al.</em> 2006 <em>emend.</em> Smith and Jones 2018" becomes "Smith <em>et al.</em>, 2018". This field is directly retrieved from the source specified in the column <code>source</code>. Moreover, accents were removed to comply with CRAN that only allows ASCII characters.</p></li>
|
||||
<li><p><code>oxygen_tolerance</code> <br> Oxygen tolerance, either <code>"aerobe"</code>, <code>"anaerobe"</code>, <code>"anaerobe/microaerophile"</code>, <code>"facultative anaerobe"</code>, <code>"likely facultative anaerobe"</code>, <code>"microaerophile"</code>, or NA. These data were retrieved from BacDive (see <em>Source</em>). Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus to guess the oxygen tolerance. Currently 68.3% of all ~39 000 bacteria in the data set contain an oxygen tolerance.</p></li>
|
||||
<li><p><code>source</code><br> Either <code>"GBIF"</code>, <code>"LPSN"</code>, <code>"Manually added"</code>, <code>"MycoBank"</code>, or <code>"manually added"</code> (see <em>Source</em>)</p></li>
|
||||
<li><p><code>lpsn</code><br> Identifier ('Record number') of List of Prokaryotic names with Standing in Nomenclature (LPSN). This will be the first/highest LPSN identifier to keep one identifier per row. For example, <em>Acetobacter ascendens</em> has LPSN Record number 7864 and 11011. Only the first is available in the <code>microorganisms</code> data set. <em><strong>This is a unique identifier</strong></em>, though available for only ~33 000 records.</p></li>
|
||||
<li><p><code>ref</code><br> Abbreviated authority citation for the nomenclatural act that established the current name combination, following ICNP conventions. For species described in their current genus (<em>sp. nov.</em>), this is the original description author(s) and year. For species transferred to a different genus (<em>comb. nov.</em>), this is the reclassification author(s) and year. Emendations are excluded. For synonyms, this is the authority under which the synonym was originally published. This field is directly retrieved from the source specified in the column <code>source</code>. Diacritics were removed to comply with CRAN, that only allows ASCII characters.</p></li>
|
||||
<li><p><code>oxygen_tolerance</code> <br> Oxygen tolerance, either <code>"aerobe"</code>, <code>"anaerobe"</code>, <code>"anaerobe/microaerophile"</code>, <code>"facultative anaerobe"</code>, <code>"likely facultative anaerobe"</code>, <code>"microaerophile"</code>, or NA. These data were retrieved from BacDive (see <em>Source</em>). Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus to guess the oxygen tolerance. Currently 1.3784 × 10<sup>6</sup>% of all 2 bacteria in the data set contain an oxygen tolerance.</p></li>
|
||||
<li><p><code>morphology</code> <br> Morphology (cell shape), either <code>"cocci"</code>, <code>"coccobacilli"</code>, <code>"filamentous"</code>, <code>"likely cocci"</code>, <code>"likely coccobacilli"</code>, <code>"likely filamentous"</code>, <code>"likely rods"</code>, <code>"likely spirilla"</code>, <code>"rods"</code>, <code>"spirilla"</code>, or NA. These data were retrieved from BacDive (see <em>Source</em>). Genera that are clinically established as coccobacilli (the HACEK group and beyond, such as <em>Haemophilus</em> and <em>Acinetobacter</em>) are classified as such regardless of BacDive majority vote. Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus. Currently 1.3232 × 10<sup>6</sup>% of all 2 bacteria in the data set contain a morphology.</p></li>
|
||||
<li><p><code>source</code><br> Either <code>"GBIF"</code>, <code>"LPSN"</code>, <code>"MycoBank"</code>, or <code>"manually added"</code> (see <em>Source</em>)</p></li>
|
||||
<li><p><code>lpsn</code><br> Identifier ('Record number') of List of Prokaryotic names with Standing in Nomenclature (LPSN). This will be the first/highest LPSN identifier to keep one identifier per row. For example, <em>Acetobacter ascendens</em> has LPSN Record number 7864 and 11011. Only the first is available in the <code>microorganisms</code> data set. <em><strong>This is a unique identifier</strong></em>, though available for only ~36 000 records.</p></li>
|
||||
<li><p><code>lpsn_parent</code><br> LPSN identifier of the parent taxon</p></li>
|
||||
<li><p><code>lpsn_renamed_to</code><br> LPSN identifier of the currently valid taxon</p></li>
|
||||
<li><p><code>mycobank</code><br> Identifier ('MycoBank #') of MycoBank. <em><strong>This is a unique identifier</strong></em>, though available for only ~19 000 records.</p></li>
|
||||
<li><p><code>mycobank</code><br> Identifier ('MycoBank #') of MycoBank. <em><strong>This is a unique identifier</strong></em>, though available for only ~25 000 records.</p></li>
|
||||
<li><p><code>mycobank_parent</code><br> MycoBank identifier of the parent taxon</p></li>
|
||||
<li><p><code>mycobank_renamed_to</code><br> MycoBank identifier of the currently valid taxon</p></li>
|
||||
<li><p><code>gbif</code><br> Identifier ('taxonID') of Global Biodiversity Information Facility (GBIF). <em><strong>This is a unique identifier</strong></em>, though available for only ~49 000 records.</p></li>
|
||||
<li><p><code>gbif</code><br> Identifier ('taxonID') of Global Biodiversity Information Facility (GBIF), via Catalogue of Life (COL). <em><strong>This is a unique identifier</strong></em>, though available for only ~79 000 records.</p></li>
|
||||
<li><p><code>gbif_parent</code><br> GBIF identifier of the parent taxon</p></li>
|
||||
<li><p><code>gbif_renamed_to</code><br> GBIF identifier of the currently valid taxon</p></li>
|
||||
<li><p><code>prevalence</code><br> Prevalence of the microorganism based on Bartlett <em>et al.</em> (2022, <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a>
|
||||
), see <code><a href="mo_matching_score.html">mo_matching_score()</a></code> for the full explanation</p></li>
|
||||
<li><p><code>snomed</code><br> Systematized Nomenclature of Medicine (SNOMED) code of the microorganism, version of July 16th, 2024 (see <em>Source</em>). Use <code><a href="mo_property.html">mo_snomed()</a></code> to retrieve it quickly, see <code><a href="mo_property.html">mo_property()</a></code>.</p></li>
|
||||
</ul></div>
|
||||
<div class="section level2">
|
||||
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
|
||||
<p>Taxonomic entries were imported in this order of importance:</p><ol><li><p>List of Prokaryotic names with Standing in Nomenclature (LPSN):<br><br>
|
||||
Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong> International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a>
|
||||
. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on June 24th, 2024.</p></li>
|
||||
<li><p>MycoBank:<br><br>
|
||||
Vincent, R <em>et al</em> (2013). <strong>MycoBank gearing up for new horizons.</strong> IMA Fungus, 4(2), 371-9; <a href="https://doi.org/10.5598/imafungus.2013.04.02.16" class="external-link">doi:10.5598/imafungus.2013.04.02.16</a>
|
||||
. Accessed from <a href="https://www.mycobank.org" class="external-link">https://www.mycobank.org</a> on June 24th, 2024.</p></li>
|
||||
<li><p>Global Biodiversity Information Facility (GBIF):<br><br>
|
||||
GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset <a href="https://doi.org/10.15468/39omei" class="external-link">doi:10.15468/39omei</a>
|
||||
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on June 24th, 2024.</p></li>
|
||||
</ol><p>Furthermore, these sources were used for additional details:</p><ul><li><p>BacDive:<br><br>
|
||||
Reimer, LC <em>et al.</em> (2022). <strong><em>BacDive</em> in 2022: the knowledge base for standardized bacterial and archaeal data.</strong> Nucleic Acids Res., 50(D1):D741-D74; <a href="https://doi.org/10.1093/nar/gkab961" class="external-link">doi:10.1093/nar/gkab961</a>
|
||||
. Accessed from <a href="https://bacdive.dsmz.de" class="external-link">https://bacdive.dsmz.de</a> on July 16th, 2024.</p></li>
|
||||
<li><p>Systematized Nomenclature of Medicine - Clinical Terms (SNOMED-CT):<br><br>
|
||||
Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12). Accessed from <a href="https://www.cdc.gov/phin/php/phinvads/" class="external-link">https://www.cdc.gov/phin/php/phinvads/</a> on July 16th, 2024.</p></li>
|
||||
<li><p>Grimont <em>et al.</em> (2007). Antigenic Formulae of the Salmonella Serovars, 9th Edition. WHO Collaborating Centre for Reference and Research on <em>Salmonella</em> (WHOCC-SALM).</p></li>
|
||||
<li><p>Bartlett <em>et al.</em> (2022). <strong>A comprehensive list of bacterial pathogens infecting humans</strong> <em>Microbiology</em> 168:001269; <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a></p></li>
|
||||
<li><p><code>snomed</code><br> Systematized Nomenclature of Medicine (SNOMED) code of the microorganism, version of 16th of July, 2024 (see <em>Source</em>). Use <code><a href="mo_property.html">mo_snomed()</a></code> to retrieve it quickly, see <code><a href="mo_property.html">mo_property()</a></code>.</p></li>
|
||||
</ul></div>
|
||||
<div class="section level2">
|
||||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||||
@@ -114,11 +96,11 @@ Public Health Information Network Vocabulary Access and Distribution System (PHI
|
||||
<h2 id="included-taxa">Included Taxa<a class="anchor" aria-label="anchor" href="#included-taxa"></a></h2>
|
||||
|
||||
|
||||
<p>Included taxonomic data from <a href="https://lpsn.dsmz.de" class="external-link">LPSN</a>, <a href="https://www.mycobank.org" class="external-link">MycoBank</a>, and <a href="https://www.gbif.org" class="external-link">GBIF</a> are:</p><ul><li><p>All ~39 000 (sub)species from the kingdoms of Archaea and Bacteria</p></li>
|
||||
<li><p>~28 000 species from the kingdom of Fungi. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package. Only relevant fungi are covered (such as all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Cryptococcus</em>, <em>Histoplasma</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
|
||||
<li><p>~8 100 (sub)species from the kingdom of Protozoa</p></li>
|
||||
<li><p>~1 600 (sub)species from 39 other relevant genera from the kingdom of Animalia (such as <em>Strongyloides</em> and <em>Taenia</em>)</p></li>
|
||||
<li><p>All ~26 000 previously accepted names of all included (sub)species (these were taxonomically renamed)</p></li>
|
||||
<p>Included taxonomic data from <a href="https://lpsn.dsmz.de" class="external-link">LPSN</a>, <a href="https://www.mycobank.org" class="external-link">MycoBank</a>, and <a href="https://www.gbif.org" class="external-link">GBIF</a> are:</p><ul><li><p>All 2 (sub)species from the kingdoms of Archaea and Bacteria</p></li>
|
||||
<li><p>~36 000 species from the kingdom of Fungi. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package. Only relevant fungi are covered (such as all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Cryptococcus</em>, <em>Histoplasma</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
|
||||
<li><p>~11 000 (sub)species from the kingdom of Protozoa</p></li>
|
||||
<li><p>~2 000 (sub)species from ~60 other relevant genera from the kingdom of Animalia (such as <em>Strongyloides</em> and <em>Taenia</em>)</p></li>
|
||||
<li><p>All ~31 000 previously accepted names of all included (sub)species (these were taxonomically renamed)</p></li>
|
||||
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
|
||||
<li><p>The identifier of the parent taxons</p></li>
|
||||
<li><p>The year and first author of the related scientific publication</p></li>
|
||||
@@ -143,6 +125,25 @@ Public Health Information Network Vocabulary Access and Distribution System (PHI
|
||||
<p>For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.</p>
|
||||
<p>Visit <a href="https://amr-for-r.org/articles/datasets.html">our website for direct download links</a>, or explore the actual files in <a href="https://github.com/msberends/AMR/tree/main/data-raw/datasets" class="external-link">our GitHub repository</a>.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
|
||||
<p>Taxonomic entries were imported in this order of importance:</p><ol><li><p>List of Prokaryotic names with Standing in Nomenclature (LPSN):<br><br>
|
||||
Freese, HM <em>et al.</em> (2026). <strong>TYGS and LPSN in 2025: a Global Core Biodata Resource for genome-based classification and nomenclature of prokaryotes within DSMZ Digital Diversity.</strong> Nucleic Acids Research, 54, D884–D891; <a href="https://doi.org/10.1093/nar/gkaf1110" class="external-link">doi:10.1093/nar/gkaf1110</a>
|
||||
. Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on 7th of May, 2026.</p></li>
|
||||
<li><p>MycoBank:<br><br>
|
||||
Vincent, R <em>et al</em> (2013). <strong>MycoBank gearing up for new horizons.</strong> IMA Fungus, 4(2), 371-9; <a href="https://doi.org/10.5598/imafungus.2013.04.02.16" class="external-link">doi:10.5598/imafungus.2013.04.02.16</a>
|
||||
. Accessed from <a href="https://www.mycobank.org" class="external-link">https://www.mycobank.org</a> on 7th of May, 2026.</p></li>
|
||||
<li><p>Global Biodiversity Information Facility (GBIF), via Catalogue of Life (COL):<br><br>
|
||||
Banki, O. <em>et al.</em> (2026). Catalogue of Life (2026-04-18 XR). Catalogue of Life Foundation, Amsterdam, Netherlands. <a href="https://doi.org/10.48580/dgxjw" class="external-link">doi:10.48580/dgxjw</a>
|
||||
. Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on 7th of May, 2026.</p></li>
|
||||
</ol><p>Furthermore, these sources were used for additional details:</p><ul><li><p>BacDive:<br><br>
|
||||
Reimer, LC <em>et al.</em> (2022). <strong><em>BacDive</em> in 2022: the knowledge base for standardized bacterial and archaeal data.</strong> Nucleic Acids Res., 50(D1):D741-D74; <a href="https://doi.org/10.1093/nar/gkab961" class="external-link">doi:10.1093/nar/gkab961</a>
|
||||
. Accessed from <a href="https://bacdive.dsmz.de" class="external-link">https://bacdive.dsmz.de</a> on 7th of May, 2026.</p></li>
|
||||
<li><p>Systematized Nomenclature of Medicine - Clinical Terms (SNOMED-CT):<br><br>
|
||||
Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12). Accessed from <a href="https://www.cdc.gov/phin/php/phinvads/" class="external-link">https://www.cdc.gov/phin/php/phinvads/</a> on 16th of July, 2024.</p></li>
|
||||
<li><p>Grimont <em>et al.</em> (2007). Antigenic Formulae of the Salmonella Serovars, 9th Edition. WHO Collaborating Centre for Reference and Research on <em>Salmonella</em> (WHOCC-SALM).</p></li>
|
||||
<li><p>Bartlett <em>et al.</em> (2022). <strong>A comprehensive list of bacterial pathogens infecting humans</strong> <em>Microbiology</em> 168:001269; <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a></p></li>
|
||||
</ul></div>
|
||||
<div class="section level2">
|
||||
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
|
||||
<div class="dont-index"><p><code><a href="as.mo.html">as.mo()</a></code>, <code><a href="mo_property.html">mo_property()</a></code>, <a href="microorganisms.groups.html">microorganisms.groups</a>, <a href="microorganisms.codes.html">microorganisms.codes</a>, <a href="intrinsic_resistant.html">intrinsic_resistant</a></p></div>
|
||||
@@ -151,25 +152,26 @@ Public Health Information Network Vocabulary Access and Distribution System (PHI
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">microorganisms</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 78,679 × 26</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo fullname status kingdom phylum class order family genus species</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">B_</span>GRAMN (unknown … unkno… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… (unk… <span style="color: #949494;">"</span>(unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">B_</span>GRAMP (unknown … unkno… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… (unk… <span style="color: #949494;">"</span>(unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">B_</span>ANAER-NEG (unknown … unkno… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… (unk… <span style="color: #949494;">"</span>(unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;">B_</span>ANAER-POS (unknown … unkno… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… (unk… <span style="color: #949494;">"</span>(unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">B_</span>ANAER (unknown … unkno… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… (unk… <span style="color: #949494;">"</span>(unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">F_</span>FUNGUS (unknown … unkno… Fungi (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… (unk… <span style="color: #949494;">"</span>(unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #BB0000;"> UNKNOWN</span> (unknown … unkno… (unkno… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… (unk… <span style="color: #949494;">"</span>(unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">P_</span>PROTOZOAN (unknown … unkno… Protoz… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… (unk… <span style="color: #949494;">"</span>(unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">F_</span>YEAST (unknown … unkno… Fungi (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… (unk… <span style="color: #949494;">"</span>(unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">F_</span>AABRN Aabaarnia unkno… Fungi Ascom… Leca… Ostr… <span style="color: #949494;">""</span> Aaba… <span style="color: #949494;">""</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 78,669 more rows</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 16 more variables: subspecies <chr>, rank <chr>, ref <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># oxygen_tolerance <chr>, source <chr>, lpsn <chr>, lpsn_parent <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># lpsn_renamed_to <chr>, mycobank <chr>, mycobank_parent <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># mycobank_renamed_to <chr>, gbif <chr>, gbif_parent <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># gbif_renamed_to <chr>, prevalence <dbl>, snomed <list></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 96,982 × 28</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo fullname status domain kingdom phylum class order family</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">B_</span>GRAMN (unknown Gr… unkno… Bacte… (unkno… (unkn… (unk… (unk… (unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">B_</span>GRAMP (unknown Gr… unkno… Bacte… (unkno… (unkn… (unk… (unk… (unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">B_</span>ANAER-NEG (unknown an… unkno… Bacte… (unkno… (unkn… (unk… (unk… (unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;">B_</span>ANAER-POS (unknown an… unkno… Bacte… (unkno… (unkn… (unk… (unk… (unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">B_</span>ANAER (unknown an… unkno… Bacte… (unkno… (unkn… (unk… (unk… (unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">F_</span>FUNGUS (unknown fu… unkno… Fungi Fungi (unkn… (unk… (unk… (unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #BB0000;"> UNKNOWN</span> (unknown na… unkno… (unkn… (unkno… (unkn… (unk… (unk… (unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">P_</span>PROTOZOAN (unknown pr… unkno… Proto… Protoz… (unkn… (unk… (unk… (unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">F_</span>YEAST (unknown ye… unkno… Fungi Fungi (unkn… (unk… (unk… (unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">B_</span>[FAM]<span style="color: #949494;">_</span>ABDTBCTR Abditibacte… accep… Bacte… Pseudo… Abdit… Abdi… Abdi… Abdit…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 96,972 more rows</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 19 more variables: genus <chr>, species <chr>, subspecies <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># rank <chr>, ref <chr>, oxygen_tolerance <chr>, morphology <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># source <chr>, lpsn <chr>, lpsn_parent <chr>, lpsn_renamed_to <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># mycobank <chr>, mycobank_parent <chr>, mycobank_renamed_to <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># gbif <chr>, gbif_parent <chr>, gbif_renamed_to <chr>, prevalence <dbl>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># snomed <list></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||||
|
||||
Reference in New Issue
Block a user